Biosystems最新文献

{"title":"Contrasting philosophical and scientific views in the long history of studying the generation of form in development","authors":"Ute Deichmann","doi":"10.1016/j.biosystems.2024.105260","DOIUrl":"10.1016/j.biosystems.2024.105260","url":null,"abstract":"<div><p>Focusing on the opposing ways of thinking of philosophers and scientists to explain the generation of form in biological development, I show that today's controversies over explanations of early development bear fundamental similarities to the dichotomy of preformation theory versus epigenesis in Greek antiquity. They are related to the acceptance or rejection of the idea of a physical form of what today would be called information for the generating of the embryo as a necessary pre-requisite for specific development and heredity.</p><p>As a recent example, I scrutinize the dichotomy of genomic causality versus self-organization in 20th and 21st century theories of the generation of form. On the one hand, the generation of patterns and form, as well as the constant outcome in development, are proposed to be causally related to something that is \"preformed\" in the germ cells, the nucleus of germ cells, or the genome. On the other hand, it is proposed that there is no pre-existing form or information, and development is seen as a process where genuinely new characters emerge from formless matter, either by immaterial \"forces of life,\" or by physical-chemical processes of self-organization.</p><p>I also argue that these different ways of thinking and the research practices associated with them are not equivalent, and maintain that it is impossible to explain the generation of form and constant outcome of development without the assumption of the transmission of pre-existing information in the form of DNA sequences in the genome. Only in this framework of \"preformed\" information can \"epigenesis\" in the form of physical and chemical processes of self-organization play an important role.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S030326472400145X/pdfft?md5=30013537308b2efd5f437abfd6fe57ba&pid=1-s2.0-S030326472400145X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Size matters in metabolic scaling: Critical role of the thermodynamic efficiency of ATP synthesis and its dependence on mitochondrial H+ leak across mammalian species","authors":"Sunil Nath","doi":"10.1016/j.biosystems.2024.105255","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105255","url":null,"abstract":"<div><p>In this last article of the trilogy, the unified biothermokinetic theory of ATP synthesis developed in the previous two papers is applied to a major problem in comparative physiology, biochemistry, and ecology—that of metabolic scaling as a function of body mass <em>across</em> species. A clear distinction is made between intraspecific and interspecific relationships in energy metabolism, clearing up confusion that had existed from the very beginning since Kleiber first proposed his mouse-to-elephant rule almost a century ago. It is shown that the overall mass exponent of basal/standard metabolic rate in the allometric relationship <span><math><mrow><mi>P</mi><mo>=</mo><msub><mi>P</mi><mn>0</mn></msub><msup><mi>M</mi><mrow><msup><mi>b</mi><mo>′</mo></msup><mo>+</mo><mi>b</mi></mrow></msup></mrow></math></span> is composed of two parts, one emerging from the relative intraspecific <em>constancy</em> of the slope (<span><math><mrow><mi>b</mi></mrow></math></span>), and the other (<span><math><mrow><msup><mi>b</mi><mo>′</mo></msup></mrow></math></span>) arising from the interspecific <em>variation</em> of the mass coefficient, <span><math><mrow><mi>a</mi><mrow><mo>(</mo><mi>M</mi><mo>)</mo></mrow></mrow></math></span> with body size. Quantitative analysis is shown to reveal the hidden underlying relationship followed by the interspecific mass coefficient, <span><math><mrow><mi>a</mi><mrow><mo>(</mo><mi>M</mi><mo>)</mo></mrow><mo>=</mo><msub><mi>P</mi><mn>0</mn></msub><msup><mi>M</mi><mn>0.10</mn></msup></mrow></math></span>, and a universal value of <span><math><mrow><msub><mi>P</mi><mn>0</mn></msub><mo>=</mo><mn>3.23</mn></mrow></math></span> watts, <span><math><mrow><mi>W</mi></mrow></math></span> is derived from empirical data on mammals from mouse to cattle. The above relationship is shown to be understood only within an evolutionary biological context, and provides a physiological explanation for Cope's rule. The analysis also helps in fundamentally understanding how variability and a diversity of scaling exponents arises in allometric relations in biology and ecology. Next, a <em>molecular-level</em> understanding of the scaling of metabolism across mammalian species is shown to be obtained by consideration of the thermodynamic efficiency of ATP synthesis <em>η</em>, taking mitochondrial proton leak as a major determinant of basal metabolic rate in biosystems. An iterative solution is obtained by solving the mathematical equations of the biothermokinetic ATP theory, and the key thermodynamic parameters, e.g. the degree of coupling <span><math><mrow><mi>q</mi></mrow></math></span>, the operative <span><math><mrow><mi>P</mi><mo>/</mo><mi>O</mi></mrow></math></span> ratio, and the metabolic efficiency of ATP synthesis <em>η</em> are quantitatively evaluated for mammals from rat to cattle. Increases in <em>η</em> (by <span><math><mrow><mo>∼</mo><mn>15</mn><mo>%</mo></mrow></math></span>) over a <span><math><mrow><mn>2000</mn><mo>−</mo></mr","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141429894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological thermodynamics: Bridging the gap between physics and life","authors":"","doi":"10.1016/j.biosystems.2024.105258","DOIUrl":"10.1016/j.biosystems.2024.105258","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001436/pdfft?md5=415e234884f9db5efc63bbaaa94c0bfe&pid=1-s2.0-S0303264724001436-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of directed quasi-metric distances for quantifying the information of gene families","authors":"","doi":"10.1016/j.biosystems.2024.105256","DOIUrl":"10.1016/j.biosystems.2024.105256","url":null,"abstract":"<div><p>A large hindrance to analyzing information in genetic or protein sequence data has been a lack of a mathematical framework for doing so. In this paper, we present a multinomial probability space <span><math><mrow><mi>X</mi></mrow></math></span> as a general foundation for multicategory discrete data, where categories refer to variants/alleles of biosequences. The external information that is infused in order to generate a sample of such data is quantified as a distance on <span><math><mrow><mi>X</mi></mrow></math></span> between the prior distribution of data and the empirical distribution of the sample. A number of distances on <span><math><mrow><mi>X</mi></mrow></math></span> are treated. All of them have an information theoretic interpretation, reflecting the information that the sampling mechanism provides about which variants that have a selective advantage and therefore appear more frequently compared to prior expectations. This includes distances on <span><math><mrow><mi>X</mi></mrow></math></span> based on mutual information, conditional mutual information, active information, and functional information. The functional information distance is singled out as particularly useful. It is simple and has intuitive interpretations in terms of 1) a rejection sampling mechanism, where functional entities are retained, whereas non-functional categories are censored, and 2) evolutionary waiting times. The functional information is also a <em>quasi-metric</em> on <span><math><mrow><mi>X</mi></mrow></math></span><strong><em>,</em></strong> with information being measured in an asymmetric, mountainous landscape. This quasi-metric property is also retained for a robustified version of the functional information distance that allows for mutations in the sampling mechanism. The functional information quasi-metric has been applied with success on bioinformatics data sets, for proteins and sequence alignment of protein families.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001412/pdfft?md5=8ca4ad1b80b24baedfa49920223c3ee7&pid=1-s2.0-S0303264724001412-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What do stimulated beta cells have in common with cancer cells?","authors":"Marko Marhl","doi":"10.1016/j.biosystems.2024.105257","DOIUrl":"10.1016/j.biosystems.2024.105257","url":null,"abstract":"<div><p>This study investigates the metabolic parallels between stimulated pancreatic beta cells and cancer cells, focusing on glucose and glutamine metabolism. Addressing the significant public health challenges of Type 2 Diabetes (T2D) and cancer, we aim to deepen our understanding of the mechanisms driving insulin secretion and cellular proliferation. Our analysis of anaplerotic cycles and the role of NADPH in biosynthesis elucidates their vital functions in both processes. Additionally, we point out that both cell types share an antioxidative response mediated by the Nrf2 signaling pathway, glutathione synthesis, and UCP2 upregulation. Notably, UCP2 facilitates the transfer of C4 metabolites, enhancing reductive TCA cycle metabolism. Furthermore, we observe that hypoxic responses are transient in beta cells post-stimulation but persistent in cancer cells. By synthesizing these insights, the research may suggest novel therapeutic targets for T2D, highlighting the shared metabolic strategies of stimulated beta cells and cancer cells. This comparative analysis not only illuminates the metabolic complexity of these conditions but also emphasizes the crucial role of metabolic pathways in cell function and survival, offering fresh perspectives for tackling T2D and cancer challenges.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001424/pdfft?md5=1e8f035d2de7eb7bed67fc9a6954be77&pid=1-s2.0-S0303264724001424-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determining cellular lineage directed networks in hematopoiesis using single-cell transcriptomic data and volatility-constrained correlation","authors":"Tomoshiro Ochiai ,&nbsp;Jose C. Nacher","doi":"10.1016/j.biosystems.2024.105248","DOIUrl":"10.1016/j.biosystems.2024.105248","url":null,"abstract":"<div><p>Single-cell transcriptome sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling the analysis of expression profiles at an individual cell level. This technology has shown promise in uncovering new cell types, gene functions, cell differentiation, and trajectory inference through the study of various biological processes, such as hematopoiesis. Recent scRNA-seq analysis of mouse bone marrow cells has provided a network model of hematopoietic lineage. However, all data analyses have predicted undirected network maps for the associated cell trajectories. Moreover, the debate regarding the origin of basophil cells still persists. In this work, we apply the Volatility Constrained (VC) correlation method to predict not only the network structure but also the causality or directionality between the cell types present in the hematopoietic process. Our findings suggest a dual origin of basophils, from both granulocyte/macrophage and erythrocyte progenitors, the latter being a trajectory less explored in previous research. The proposed approach and predictions may assist in developing a complete hematopoietic process map, impacting our understanding of hematopoiesis and providing a robust directional network framework for further biomedical research.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermodynamic model for memory","authors":"Qinyi Zhao","doi":"10.1016/j.biosystems.2024.105247","DOIUrl":"10.1016/j.biosystems.2024.105247","url":null,"abstract":"<div><p>A thermodynamic model for memory formation is proposed. Key points include: 1) Any thought or consciousness corresponds to a thermodynamic system of nerve cells. 2) The system concept of nerve cells can only be described by thermodynamics of condensed matter. 3) The memory structure is logically associated with the system structure or the normal structure of biology. 4) The development of our thoughts is processed irreversibly, and numerous states or thoughts can be generated. 5) Memory formation results from the reorganization and change of cellular structures (or memory structures), which are related to nerve cell skeleton and membrane. Their alteration can change the excitability of nerve cells and the pathway of neural impulse conduction. 6) Amnesia results from the loss of thermodynamic stability of the memory structure, which can be achieved by different ways. Some related phenomena and facts are discussed. The analysis shows that thermodynamics can account for the basic properties of memory.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effective identification and differential analysis of anticancer peptides","authors":"Lichao Zhang ,&nbsp;Xueli Hu ,&nbsp;Kang Xiao ,&nbsp;Liang Kong","doi":"10.1016/j.biosystems.2024.105246","DOIUrl":"10.1016/j.biosystems.2024.105246","url":null,"abstract":"<div><p>Anticancer peptides (ACPs) have recently emerged as promising cancer therapeutics due to their selectivity and lower toxicity. However, the number of experimentally validated ACPs is limited, and identifying ACPs from large-scale sequence data is time-consuming and expensive. Therefore, it is critical to develop and improve upon existing computational models for identifying ACPs. In this study, a computational method named ACP_DA was proposed based on peptide residue composition and physiochemical properties information. To curtail overfitting and reduce computational costs, a sequential forward selection method was utilized to construct the optimal feature groups. Subsequently, the feature vectors were fed into light gradient boosting machine classifier for model construction. It was observed by an independent set test that ACP_DA achieved the highest Matthew's correlation coefficient of 0.63 and accuracy of 0.8129, displaying at least a 2% enhancement compared to state-of-the-art methods. The satisfactory results demonstrate the effectiveness of ACP_DA as a powerful tool for identifying ACPs, with the potential to significantly contribute to the development and optimization of promising therapies. The data and resource codes are available at <span>https://github.com/Zlclab/ACP_DA</span><svg><path></path></svg>.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aggregate Boid behavior to aid in artificial autopoietic organization","authors":"Steven Lawrence,&nbsp;Chrystopher L. Nehaniv","doi":"10.1016/j.biosystems.2024.105245","DOIUrl":"10.1016/j.biosystems.2024.105245","url":null,"abstract":"<div><p>Analyzing carbon-based life on earth can lead to biased inferences on the nature of life as might exist in elsewhere in the universe in alternative forms, therefore, scientists have looked into either abstracting life into constituent systems it is comprised of, or logics of life, or lists of essential criteria, or essential dynamic patterning that characterizes the living. A system-level characterization that is and referred to as a general pattern of minimal life is <em>autopoiesis</em> (Varela et al., 1974) including production, maintenance and replacement of required constituents for setting up and maintaining an internal environment with self/other separation that regulates and is constitutive of processes that produce the environment and components for processes that comprise this ongoing activity of self-production in ‘recursively’, i.e., in a manner that allows the organizational pattern to continually reconstitute the conditions, components and processes required for its own perpetuation. This seminal concept of an autopoiesis is instantiated in life as we know it, but might also be instantiated in different media and in unforeseen ways. Other researchers have argued life is more than autopoiesis and that it is a co-emergent property of autopoiesis and cognition. Life produces many emergent properties such as synchronization and patterns as seen in flocks and herds of different animal species. The mechanics of this synchrony displayed in flocks and herd animals has been extracted by Craig Reynolds into a generative model referred to as “Boids”. With these concepts in mind, we address the following research question: How can the synchronous maneuvers and aggregate behavior of Boids contribute to constitutive subsystems in realizing an autopoietic system? Can such a system exhibit minimal cognition? This work attempts to answer these questions with a bottom-up approach to constructing an artificial life system. We exhibit a computational model of autopoiesis and a minimal level of cognition in the sense of M. Bitbol and P. Luigi Luisi, whereby an autopoietic entity engages in active assimilation of external components as part of its activity of self-production.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0303264724001308/pdfft?md5=c05922d2f995dec110768bea2047e4cc&pid=1-s2.0-S0303264724001308-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141238779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of avian eggshell membrane structure on microbial penetration: A simulation study","authors":"Seungwoo Sim ,&nbsp;Cheol-Min Park ,&nbsp;Sang-Hee Lee ,&nbsp;Haeun Cho ,&nbsp;Youngheum Ji ,&nbsp;Heeso Noh ,&nbsp;Sang-im Lee","doi":"10.1016/j.biosystems.2024.105234","DOIUrl":"10.1016/j.biosystems.2024.105234","url":null,"abstract":"<div><p>Avian eggshells exhibit excellent antimicrobial properties. In this study, we conducted simulation experiments to explore the defense mechanisms of eggshell membranes with regards to their physical features. We developed a mathematical model for the movement of microorganisms and estimated their penetration ratio into eggshell membranes based on several factors, including membrane thickness, microbial size, directional drift, and attachment probability to membrane fibers. These results not only suggest that an eggshell membrane with multiple layers and low porosity indicates high antimicrobial performance, but also imply that the fibrous network structure of the membrane might contribute to effective defense. Our simulation results aligned with experimental findings, specifically in measuring the penetration time of <em>Escherichia coli</em> through the eggshell membrane. We briefly discuss the significance and limitations of this pilot study, as well as the potential for these results, to serve as a foundation for the development of antimicrobial materials.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}